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Biodiversity of infectious systems: from gene to ecosystem

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Axis: "Methods and algorithms for the comprehension of infectious systems"


Coordinator: François CHEVENET


This project targets the computing of methods and algorithms for the development of bioinformatic tools in order to answer fundamental biologogical and epidemiological questions. Indeed, in all research topics, we need more and more bioinformatic tools adapted to the diversity, quality and quantity of collected data, of either biological, molecular, phenotypic or epidemiological type. The information stored constantly evolve and the analyses require adapted methodological developments, allowing a rapid and easy processing of great amount of data.  

The first topic of this axis deals with the development of bioinformatic and phylogenetic methods dedicated to the evolutive and epidemiological study of infectious diseases. These methods aim for the processing of molecular data in a genomic and evolutive point of vue and to look at them against intrinsic or extrinsic data linked to the studied organisms.


The objective of the second topic is to create programs for image treatment to automatically detect morphological caracteristics (i.e. insect wings) or automatic counting, a long and hard although essential step in numerous fields in biology (counting of eggs, larva, parasites,...). The produced softwares will be adjustable by the user to allow an adaptation to other biological models.


Group members

'MiVEGEC' publications by members of the group since 2005:

| 2005 | | 2006 | | 2007 | | 2008 | | 2009 | | 2010 | | 2012 | | 2013 | | 2014 | | 2015 | | 2016 | | 2017 | | 2018 |


Berry V, Chevenet F, Doyon JP, Jousselin E (2018) A geography-aware reconciliation method to investigate diversification patterns in host/parasite interactions. Molecular Ecology Resources 18: 1173-1184 doi

Duchemin W, Gence G, Chifolleau AMA, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davin AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szollosi G, Zhang LX, Tannier E, Daubin V (2018) RecPhyloXML: a format for reconciled gene trees. Bioinformatics 34: 3646-3652 doi


Pigott DM, Golding N, Messina JP, Battle KE, Duda KA, Balard Y, Bastien P, Pratlong F, Brownstein JS, Freifeld CC, Mekaru SR, Madoff LC, George DB, Myers MF, Hay SI (2014) Global database of leishmaniasis occurrence locations, 1960-2012. Scientific Data 1: 140036 doi


Chevenet F, Doyon JP, Scornavacca C, Jacox E, Jousselin E, Berry V (2016) SylvX: a viewer for phylogenetic tree reconciliations. Bioinformatics 32: 608-613 doi

Pratlong F, Balard Y, Lami P, Talignani L, Ravel C, Dereure J, Lefebvre M, Serres G, Bastien P, Dedet JP (2016) The Montpellier Leishmania collection, from a laboratory collection to a biological resource center: a 39-year-long story. Biopreservation and Biobanking 14: 470-479 doi

Stanojcic S, Sollelis L, Kuk N, Crobu L, Balard Y, Schwob E, Bastien P, Pagès M, Sterkers Y (2016) Single-molecule analysis of DNA replication reveals novel features in the divergent eukaryotes Leishmania and Trypanosoma brucei versus mammalian cells. Scientific Reports 6: 23142 doi


Mourad R, Chevenet F, Dunn DT, Fearnhill E, Delpech V, Asboe D, Gascuel O, Hue S (2015) A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK. AIDS 29: 1917-1925 doi


Bourgeois N, Laurens C, Bertout S, Balard Y, Krasteva D, Rispail P & Lachaud L (2014) Assessment of caspofungin susceptibility of Candida glabrata by the Etest (R), CLSI, and EUCAST methods, and detection of FKS1 and FKS2 mutations. European Journal of Clinical Microbiology & Infectious Diseases. 33: 1247-1252 doi

Fiorini N, Lefort V, Chevenet F, Berry V & Chifolleau AMA (2014) CompPhy: a web-based collaborative platform for comparing phylogenies. BMC Evolutionary Biology. 14: 253 doi

Pigott DM, Bhatt S, Golding N, Duda KA, Battle KE, Brady OJ, Messina JP, Balard Y, Bastien P, Pratlong F, Brownstein JS, Freifeld C, Mekaru SR, Gething PW, George DB, Myers MF, Reithinger R & Hay SI (2014) Global distribution maps of the Leishmaniases. Elife. 3: e02851 doi

Yazdanparast E, Dos Anjos A, Garcia D, Loeuillet C, Shahbazkia HR & Vergnes B (2014) INsPECT, an open-source and versatile software for automated quantification of (Leishmania) Intracellular Parasites. PLoS Neglected Tropical Diseases. 8: e2850 doi


Al-Tam F, Adam H, dos Anjos A, Lorieux M, Larmande P, Ghesquiere A, Jouannic S & Shahbazkia HR (2013) P-TRAP: a Panicle Trait Phenotyping tool. BMC Plant Biology. 13: 122 doi

Chevenet F, Jung M, Peeters M, de Oliveira T & Gascuel O (2013) Searching for virus phylotypes. Bioinformatics. 29: 561-570 doi

El Baidouri F, Diancourt L, Berry V, Chevenet F, Pratlong F, Marty P & Ravel C (2013) Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us. PLoS Neglected Tropical Diseases. 7: e2255 doi

Jousselin E, Cruaud A, Genson G, Chevenet F, Foottit RG & Coeur d'Acier A (2013) Is ecological speciation a major trend in aphids? Insights from a molecular phylogeny of the conifer-feeding genus Cinara. Frontiers in Zoology. 10: 56 doi

Pratlong F, Lami P, Ravel C, Balard Y, Dereure J, Serres G, El Baidouri F & Dedet JP (2013) Geographical distribution and epidemiological features of Old World Leishmania infantum and Leishmania donovani foci, based on the isoenzyme analysis of 2277 strains. Parasitology. 140: 423-434 doi


Al-Tam F, Brunel AS, Bouzinbi N, Corne P, Bañuls AL & Shahbazkia HR (2012) DNAGear- a free software for spa type identification in Staphylococcus aureus. BMC Research Notes. 5: 642-642 doi

Boissière A, Tchioffo MT, Bachar D, Abate L, Marie A, Nsango SE, Shahbazkia HR, Awono-Ambene PH, Levashina EA, Christen R & Morlais I (2012) Midgut microbiota of the malaria mosquito vector Anopheles gambiae and interactions with Plasmodium falciparum infection. PLoS Pathogens. 8: e1002742 doi

Mollahosseini A, Rossignol M, Pennetier C, Cohuet A, dos Anjos A, Chandre F & Shahbazkia HR (2012) A user-friendly software to easily count Anopheles egg batches. Parasites & Vectors. 5: 122 doi [- download -] pdf


Chevenet F, Croce O, Hebrard M, Christen R & Berry V (2010) ScripTree: scripting phylogenetic graphics. Bioinformatics. 26: 1125-1126


Dereure J, Vanwambeke SO, Male P, Martinez S, Pratlong F, Balard Y & Dedet JP (2009) The potential effects of global warming on changes in canine leishmaniasis in a focus outside the classical area of the disease in southern France. Vector-Borne and Zoonotic Diseases. 9: 687-694

Pratlong F, Dereure J, Ravel C, Lami P, Balard Y, Serres G, Lanotte G, Rioux JA & Dedet JP (2009) Geographical distribution and epidemiological features of Old World cutaneous leishmaniasis foci, based on the isoenzyme analysis of 1048 strains. Tropical Medicine & International Health. 14: 1071-1085


Croce O, Chevenet F & Christen R (2008) OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences. Nucleic Acids Research. 36: W154-W156

Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM & Gascuel O (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Research. 36: W465-W469 [- phylogeny.fr -]


Godreuil S, Torrea G, Terru D, Chevenet F, Diagbouga S, Supply P, van de Perre P, Carriere C & Bañuls AL (2007) First molecular epidemiology study of Mycobacterium tuberculosis in Burkina Faso. Journal of Clinical Microbiology. 45: 921-927 pdf


Baudot A, Martin D, Mouren P, Chevenet F, Guenoche A, Jacq B & Brun C (2006) PRODISTIN Web Site: a tool for the functional classification of proteins from interaction networks. Bioinformatics. 22: 248-250

Biron DG, Brun C, Lefèvre T, Lebarbenchon C, Loxdale HD, Chevenet F, Brizard JP & Thomas F (2006) The pitfalls of proteomics experiments without the correct use of bioinformatics tools. Proteomics. 6: 5577-5596 pdf

Chevenet F, Brun C, Bañuls AL, Jacq B & Christen R (2006) TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics. 7: 439 pdf


Simon O, Chevenet F, Williams T, Caballero P & Lopez-Ferber M (2005) Physical and partial genetic map of Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV) genome. Virus Genes. 30: 403-417